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authorHao Chen2019-05-21 16:25:17 -0500
committerHao Chen2019-05-21 16:25:17 -0500
commite87aa54962f20d93e3cea18f425bb3f820768e63 (patch)
tree68d8143ede14baad5a21ec446a70318121700c70
parent3dba78248d81fc97d5347fa167828ba3a8f95cd8 (diff)
downloadgenecup-e87aa54962f20d93e3cea18f425bb3f820768e63.tar.gz
progress bar for gene_topGene search
-rwxr-xr-xserver.py132
-rw-r--r--templates/progress.html12
2 files changed, 89 insertions, 55 deletions
diff --git a/server.py b/server.py
index a54dab2..24476c6 100755
--- a/server.py
+++ b/server.py
@@ -36,7 +36,7 @@ def progress():
# generate a unique session ID to track the results
tf_path=tempfile.gettempdir()
session['path']=tf_path+"/tmp" + ''.join(random.choice(string.ascii_letters) for x in range(6))
- return render_template('progress.html')
+ return render_template('progress.html', url_in="search", url_out="cytoscape")
@app.route("/search")
def search():
@@ -81,9 +81,10 @@ def search():
# gwas
e4=searchArchived('gwas', gene)
geneEdges=e0+e1+e2+e3+e4
+ ## there is a bug here. zero link notes are not excluded anymore
if len(geneEdges) >1:
edges+=geneEdges
- nodes+="{ data: { id: '" + gene + "', nodecolor:'#E74C3C', fontweight:700, url:'/gene_gene?gene="+gene+"'} },\n"
+ nodes+="{ data: { id: '" + gene + "', nodecolor:'#E74C3C', fontweight:700, url:'/startGeneGene?forTopGene="+gene+"'} },\n"
else:
nodesToHide+=gene + " "
sentences+=sent0+sent1+sent2+sent3
@@ -140,56 +141,89 @@ def shownode():
out="<p>"+node.upper()+"<hr><li>"+ allnodes[node].replace("|", "<li>")
return render_template('sentences.html', sentences=out+"<p>")
-@app.route("/gene_gene")
+@app.route("/startGeneGene")
+def startGeneGene():
+ session['forTopGene']=request.args.get('forTopGene')
+ return render_template('progress.html', url_in="searchGeneGene", url_out="showGeneTopGene")
+
+@app.route("/searchGeneGene")
def gene_gene():
- query=request.args.get("gene")
tmp_ggPMID=session['path']+"_ggPMID"
- os.system("esearch -db pubmed -query \"" + query + "\" | efetch -format uid |sort >" + tmp_ggPMID)
- abstracts=os.popen("comm -1 -2 topGene_uniq.pmid " + tmp_ggPMID + " |fetch-pubmed -path "+pubmed_path+ " | xtract -pattern PubmedArticle -element MedlineCitation/PMID,ArticleTitle,AbstractText|sed \"s/-/ /g\"").read()
- os.system("rm "+tmp_ggPMID)
- topGenes=dict()
- out=str()
- hitGenes=dict()
- with open("./topGene_symb_alias.txt", "r") as top_f:
- for line in top_f:
- (symb, alias)=line.strip().split("\t")
- topGenes[symb]=alias.replace("; ","|")
- for row in abstracts.split("\n"):
- tiab=row.split("\t")
- pmid = tiab.pop(0)
- tiab= " ".join(tiab)
- sentences = sent_tokenize(tiab)
- ## keep the sentence only if it contains the gene
- for sent in sentences:
- if findWholeWord(query)(sent):
- sent=re.sub(r'\b(%s)\b' % query, r'<strong>\1</strong>', sent, flags=re.I)
- for symb in topGenes:
- allNames=symb+"|"+topGenes[symb]
- if findWholeWord(allNames)(sent) :
- sent=sent.replace("<b>","").replace("</b>","")
- sent=re.sub(r'\b(%s)\b' % allNames, r'<b>\1</b>', sent, flags=re.I)
- out+=query+"\t"+"gene\t" + symb+"\t"+pmid+"\t"+sent+"\n"
- if symb in hitGenes.keys():
- hitGenes[symb]+=1
- else:
- hitGenes[symb]=1
gg_file=session['path']+"_ggSent" #gene_gene
- with open(gg_file, "w+") as gg:
- gg.write(out)
- gg.close()
- results="<h4>"+query+" vs top addiction genes</h4> Click on the number of sentences will show those sentences. Click on the <span style=\"background-color:#FcF3cf\">top addiction genes</span> will show an archived search for that gene.<hr>"
- topGeneHits={}
- for key in hitGenes.keys():
- url=gg_file+"|"+query+"|"+key
- if hitGenes[key]==1:
- sentword="sentence"
- else:
- sentword="sentences"
- topGeneHits[ "<li> <a href=/sentences?edgeID=" + url+ " target=_new>" + "Show " + str(hitGenes[key]) + " " + sentword +" </a> about "+query+" and <a href=/showTopGene?topGene="+key+" target=_gene><span style=\"background-color:#FcF3cf\">"+key+"</span></a>" ]=hitGenes[key]
- topSorted = [(k, topGeneHits[k]) for k in sorted(topGeneHits, key=topGeneHits.get, reverse=True)]
- for k,v in topSorted:
- results+=k
- return render_template("sentences.html", sentences=results+"<p><br>")
+ result_file=session['path']+"_ggResult"
+ def generate(query):
+ progress=1
+ yield "data:"+str(progress)+"\n\n"
+ os.system("esearch -db pubmed -query \"" + query + "\" | efetch -format uid |sort >" + tmp_ggPMID)
+ abstracts=os.popen("comm -1 -2 topGene_uniq.pmid " + tmp_ggPMID + " |fetch-pubmed -path "+pubmed_path+ " | xtract -pattern PubmedArticle -element MedlineCitation/PMID,ArticleTitle,AbstractText|sed \"s/-/ /g\"").read()
+ os.system("rm "+tmp_ggPMID)
+ progress=10
+ yield "data:"+str(progress)+"\n\n"
+ topGenes=dict()
+ out=str()
+ hitGenes=dict()
+ with open("topGene_symb_alias.txt", "r") as top_f:
+ for line in top_f:
+ (symb, alias)=line.strip().split("\t")
+ topGenes[symb]=alias.replace("; ","|")
+ allAbstracts= abstracts.split("\n")
+ abstractCnt=len(allAbstracts)
+ rowCnt=0
+ for row in allAbstracts:
+ rowCnt+=1
+ if rowCnt/10==int(rowCnt/10):
+ progress=10+round(rowCnt/abstractCnt,2)*80
+ yield "data:"+str(progress)+"\n\n"
+ tiab=row.split("\t")
+ pmid = tiab.pop(0)
+ tiab= " ".join(tiab)
+ sentences = sent_tokenize(tiab)
+ ## keep the sentence only if it contains the gene
+ for sent in sentences:
+ if findWholeWord(query)(sent):
+ sent=re.sub(r'\b(%s)\b' % query, r'<strong>\1</strong>', sent, flags=re.I)
+ for symb in topGenes:
+ allNames=symb+"|"+topGenes[symb]
+ if findWholeWord(allNames)(sent) :
+ sent=sent.replace("<b>","").replace("</b>","")
+ sent=re.sub(r'\b(%s)\b' % allNames, r'<b>\1</b>', sent, flags=re.I)
+ out+=query+"\t"+"gene\t" + symb+"\t"+pmid+"\t"+sent+"\n"
+ if symb in hitGenes.keys():
+ hitGenes[symb]+=1
+ else:
+ hitGenes[symb]=1
+ progress=95
+ yield "data:"+str(progress)+"\n\n"
+ with open(gg_file, "w+") as gg:
+ gg.write(out)
+ gg.close()
+ results="<h4>"+query+" vs top addiction genes</h4> Click on the number of sentences will show those sentences. Click on the <span style=\"background-color:#FcF3cf\">top addiction genes</span> will show an archived search for that gene.<hr>"
+ topGeneHits={}
+ for key in hitGenes.keys():
+ url=gg_file+"|"+query+"|"+key
+ if hitGenes[key]==1:
+ sentword="sentence"
+ else:
+ sentword="sentences"
+ topGeneHits[ "<li> <a href=/sentences?edgeID=" + url+ " target=_new>" + "Show " + str(hitGenes[key]) + " " + sentword +" </a> about "+query+" and <a href=/showTopGene?topGene="+key+" target=_gene><span style=\"background-color:#FcF3cf\">"+key+"</span></a>" ]=hitGenes[key]
+ topSorted = [(k, topGeneHits[k]) for k in sorted(topGeneHits, key=topGeneHits.get, reverse=True)]
+ for k,v in topSorted:
+ results+=k
+ saveResult=open(result_file, "w+")
+ saveResult.write(results)
+ saveResult.close()
+ progress=100
+ yield "data:"+str(progress)+"\n\n"
+ ## start the run
+ query=session['forTopGene']
+ return Response(generate(query), mimetype='text/event-stream')
+
+@app.route('/showGeneTopGene')
+def showGeneTopGene ():
+ with open(session['path']+"_ggResult", "r") as result_f:
+ results=result_f.read()
+ return render_template('sentences.html', sentences=results+"<p><br>")
+
## generate a page that lists all the top 150 addiction genes with links to cytoscape graph.
@app.route("/allTopGenes")
diff --git a/templates/progress.html b/templates/progress.html
index e881a90..ff9a65f 100644
--- a/templates/progress.html
+++ b/templates/progress.html
@@ -6,12 +6,12 @@
<script>
-var r = Math.floor(Math.random() * Math.floor(100));
-var g = Math.floor(Math.random() * Math.floor(100));
-var b = Math.floor(Math.random() * Math.floor(100));
+var r = Math.floor(Math.random() * Math.floor(200));
+var g = Math.floor(Math.random() * Math.floor(200));
+var b = Math.floor(Math.random() * Math.floor(200));
document.body.style.backgroundColor = 'rgba('+r+','+g+','+b+',0.1)'
-var source = new EventSource("/search");
+var source = new EventSource("/{{url_in}}");
source.onmessage = function(event) {
$('.progress-bar').css('width', event.data+'%').attr('aria-valuenow', event.data);
$('.progress-bar-label').text(event.data+'%');
@@ -19,13 +19,13 @@ source.onmessage = function(event) {
document.body.style.backgroundColor = 'rgba('+r+','+g+','+b+',0.3)'.replace(/[^,]+(?=\))/, alpha)
if(event.data == 100){
- window.location.replace("/cytoscape")
+ window.location.replace("/{{url_out}}")
source.close()
}
}
</script>
<br>
-<b> We hope this won't take too long ... </b>
+<b> I am handling all your work while you are watching this progress bar ... </b>
<div id="progs" class="progress" style="width: 50%; margin: 50px;">
<div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 0%">
<span class="progress-bar-label">0%</span>